I figured it would be no contest, after all Samus is intimately familiar with every weakness her own power armor has, besides the roof of the ship isn't exactly the best platform for a fight, especially when Samus' suit can fly while Nack's can't.

Yeah...
No contest.
Even if they had fought, she's beaten Dark Samus, SA-X, that thing at the end of Prime Hunters, Master Chief, she's fought so many clones of herself that one more wouldn't prove much of a deal.

While i agree with arc on most of that, the Master Chief one is fanwork, so it's not cannon.
Besides, her evil counterparts have always been her toughest opponents and nack is dangerous even without the suit.

And with Adam and Duo in her suit Samus DOES have a clear advantage in the cyberwarfare department...